X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FPreferences.java;h=78a21c82c2e0d5a1f57ffd9eb6b4a8a0a657a06a;hb=a83adb45bdf9554e270921b4baad94defd314b36;hp=6d94687c15a17560ca0ab822b647c8441b6d020a;hpb=27929c642502f19a8f62b1286c7542bb87c35e18;p=jalview.git
diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 6d94687..b1206a2 100755
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -1,34 +1,79 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import javax.swing.*;
-
-import jalview.bin.*;
-import jalview.io.*;
-import jalview.jbgui.*;
-import jalview.schemes.*;
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.bin.Cache;
+import jalview.gui.Help.HelpId;
+import jalview.gui.StructureViewer.ViewerType;
+import jalview.io.BackupFiles;
+import jalview.io.FileFormatI;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.jbgui.GPreferences;
+import jalview.jbgui.GSequenceLink;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemes;
+import jalview.schemes.ResidueColourScheme;
+import jalview.urls.UrlLinkTableModel;
+import jalview.urls.api.UrlProviderFactoryI;
+import jalview.urls.api.UrlProviderI;
+import jalview.urls.desktop.DesktopUrlProviderFactory;
+import jalview.util.BrowserLauncher;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.util.UrlConstants;
+import jalview.ws.sifts.SiftsSettings;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseEvent;
+import java.io.File;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.help.HelpSetException;
+import javax.swing.JComboBox;
+import javax.swing.JFileChooser;
+import javax.swing.JInternalFrame;
+import javax.swing.JPanel;
+import javax.swing.ListSelectionModel;
+import javax.swing.RowFilter;
+import javax.swing.RowSorter;
+import javax.swing.SortOrder;
+import javax.swing.event.DocumentEvent;
+import javax.swing.event.DocumentListener;
+import javax.swing.event.ListSelectionEvent;
+import javax.swing.event.ListSelectionListener;
+import javax.swing.table.TableCellRenderer;
+import javax.swing.table.TableColumn;
+import javax.swing.table.TableModel;
+import javax.swing.table.TableRowSorter;
+
+import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
/**
* DOCUMENT ME!
@@ -36,120 +81,280 @@ import jalview.schemes.*;
* @author $author$
* @version $Revision$
*/
+@SuppressWarnings("serial")
public class Preferences extends GPreferences
{
+ public static final String ADD_SS_ANN = "ADD_SS_ANN";
+
+ public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
+
+ public static final String ALLOW_UNPUBLISHED_PDB_QUERYING = "ALLOW_UNPUBLISHED_PDB_QUERYING";
+
+ public static final String ANNOTATIONCOLOUR_MAX = "ANNOTATIONCOLOUR_MAX";
+
+ public static final String ANNOTATIONCOLOUR_MIN = "ANNOTATIONCOLOUR_MIN";
+
+ public static final String ANTI_ALIAS = "ANTI_ALIAS";
+
+ public static final String AUTO_CALC_CONSENSUS = "AUTO_CALC_CONSENSUS";
+
+ public static final String AUTOASSOCIATE_PDBANDSEQS = "AUTOASSOCIATE_PDBANDSEQS";
+
+ public static final String CENTRE_COLUMN_LABELS = "CENTRE_COLUMN_LABELS";
+
+ public static final String CHIMERA_PATH = "CHIMERA_PATH";
+
+ public static final String DBREFFETCH_USEPICR = "DBREFFETCH_USEPICR";
+
+ public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
+
+ public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
+
+ public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
+
+ public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
+
+ public static final String FIGURE_AUTOIDWIDTH = "FIGURE_AUTOIDWIDTH";
+
+ public static final String FIGURE_FIXEDIDWIDTH = "FIGURE_FIXEDIDWIDTH";
+
+ public static final String FOLLOW_SELECTIONS = "FOLLOW_SELECTIONS";
+
+ public static final String FONT_NAME = "FONT_NAME";
+
+ public static final String FONT_SIZE = "FONT_SIZE";
+
+ public static final String FONT_STYLE = "FONT_STYLE";
+
+ public static final String GAP_COLOUR = "GAP_COLOUR";
+
+ public static final String GAP_SYMBOL = "GAP_SYMBOL";
+
+ public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR";
+
+ public static final String HIDE_INTRONS = "HIDE_INTRONS";
+
+ public static final String ID_ITALICS = "ID_ITALICS";
+
+ public static final String ID_ORG_HOSTURL = "ID_ORG_HOSTURL";
+
+ public static final String MAP_WITH_SIFTS = "MAP_WITH_SIFTS";
+
+ public static final String NOQUESTIONNAIRES = "NOQUESTIONNAIRES";
+
+ public static final String NORMALISE_CONSENSUS_LOGO = "NORMALISE_CONSENSUS_LOGO";
+
+ public static final String NORMALISE_LOGO = "NORMALISE_LOGO";
+
+ public static final String PAD_GAPS = "PAD_GAPS";
+
+ public static final String PDB_DOWNLOAD_FORMAT = "PDB_DOWNLOAD_FORMAT";
+
+ public static final String QUESTIONNAIRE = "QUESTIONNAIRE";
+
+ public static final String RELAXEDSEQIDMATCHING = "RELAXEDSEQIDMATCHING";
+
+ public static final String RIGHT_ALIGN_IDS = "RIGHT_ALIGN_IDS";
+
+ public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
+
+ public static final String SHOW_ANNOTATIONS = "SHOW_ANNOTATIONS";
+
+ public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
+
+ public static final String SHOW_CONSENSUS = "SHOW_CONSENSUS";
+
+ public static final String SHOW_CONSENSUS_HISTOGRAM = "SHOW_CONSENSUS_HISTOGRAM";
+
+ public static final String SHOW_CONSENSUS_LOGO = "SHOW_CONSENSUS_LOGO";
+
+ public static final String SHOW_CONSERVATION = "SHOW_CONSERVATION";
+
+ public static final String SHOW_DBREFS_TOOLTIP = "SHOW_DBREFS_TOOLTIP";
+
+ public static final String SHOW_GROUP_CONSENSUS = "SHOW_GROUP_CONSENSUS";
+
+ public static final String SHOW_GROUP_CONSERVATION = "SHOW_GROUP_CONSERVATION";
+
+ public static final String SHOW_JVSUFFIX = "SHOW_JVSUFFIX";
+
+ public static final String SHOW_NPFEATS_TOOLTIP = "SHOW_NPFEATS_TOOLTIP";
+
+ public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY";
+
+ public static final String SHOW_OV_HIDDEN_AT_START = "SHOW_OV_HIDDEN_AT_START";
+
+ public static final String SHOW_OVERVIEW = "SHOW_OVERVIEW";
+
+ public static final String SHOW_QUALITY = "SHOW_QUALITY";
+
+ public static final String SHOW_UNCONSERVED = "SHOW_UNCONSERVED";
+
+ public static final String SORT_ALIGNMENT = "SORT_ALIGNMENT";
+
+ public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
+
+ public static final String SORT_BY_TREE = "SORT_BY_TREE";
+
+ public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
+
+ public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
+
+ public static final String STRUCTURE_DIMENSIONS = "STRUCTURE_DIMENSIONS";
+
+ public static final String UNIPROT_DOMAIN = "UNIPROT_DOMAIN";
+
+ public static final String USE_FULL_SO = "USE_FULL_SO";
+
+ public static final String USE_LEGACY_GAP = "USE_LEGACY_GAP";
+
+ public static final String USE_RNAVIEW = "USE_RNAVIEW";
+
+ public static final String USER_DEFINED_COLOURS = "USER_DEFINED_COLOURS";
+
+ public static final String WRAP_ALIGNMENT = "WRAP_ALIGNMENT";
+
+
+ private static final int MIN_FONT_SIZE = 1;
+
+ private static final int MAX_FONT_SIZE = 30;
/**
* Holds name and link separated with | character. Sequence ID must be
* $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
*/
- public static Vector sequenceURLLinks;
+ public static UrlProviderI sequenceUrlLinks; // must be nonfinal for test
+
+ public final static UrlLinkTableModel dataModel;
+
/**
- * Holds name and link separated with | character. Sequence IDS and Sequences must be
- * $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$
- * and separation character for first and second token specified after a pipe character at end |,|.
+ * Holds name and link separated with | character. Sequence IDS and Sequences
+ * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
+ * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
+ * for first and second token specified after a pipe character at end |,|.
* (TODO: proper escape for using | to separate ids or sequences
*/
- public static Vector groupURLLinks;
+ public static final List groupURLLinks; // not implemented
+
+ public static final String BLOSUM62_PCA_FOR_NUCLEOTIDE = "BLOSUM62_PCA_FOR_NUCLEOTIDE";
+
+ public static final String SHOW_IDENTITY = "SHOW_IDENTITY";
+
+ public static final String SHOW_FULLSCREEN = "SHOW_FULLSCREEN";
+
+ public static final Dimension DEFAULT_STRUCTURE_DIMENSIONS = new Dimension(
+ 600, 600);
+
static
{
- String string = Cache
- .getDefault(
- "SEQUENCE_LINKS",
- "SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
- sequenceURLLinks = new Vector();
-
- try
+ // get links selected to be in the menu (SEQUENCE_LINKS)
+ // and links entered by the user but not selected (STORED_LINKS)
+ String inMenuString = Cache.getDefault("SEQUENCE_LINKS", "");
+ String notInMenuString = Cache.getDefault("STORED_LINKS", "");
+ String defaultUrl = Cache.getDefault("DEFAULT_URL",
+ UrlConstants.DEFAULT_LABEL);
+
+ // if both links lists are empty, add the DEFAULT_URL link
+ // otherwise we assume the default link is in one of the lists
+ if (inMenuString.isEmpty() && notInMenuString.isEmpty())
{
- StringTokenizer st = new StringTokenizer(string, "|");
- while (st.hasMoreElements())
- {
- String name = st.nextToken();
- String url = st.nextToken();
- // check for '|' within a regex
- int rxstart = url.indexOf("$SEQUENCE_ID$");
- while (rxstart == -1 && url.indexOf("/=$") == -1)
- {
- url = url + "|" + st.nextToken();
- }
- sequenceURLLinks.addElement(name + "|" + url);
- }
- } catch (Exception ex)
- {
- System.out.println(ex + "\nError parsing sequence links");
+ inMenuString = UrlConstants.DEFAULT_STRING;
}
+ UrlProviderFactoryI factory = new DesktopUrlProviderFactory(defaultUrl,
+ inMenuString, notInMenuString);
+ sequenceUrlLinks = factory.createUrlProvider();
+ dataModel = new UrlLinkTableModel(sequenceUrlLinks);
+
/**
- * TODO: reformulate groupURL encoding so two or more can be stored in the .properties file as '|' separated strings
+ * TODO: reformulate groupURL encoding so two or more can be stored in the
+ * .properties file as '|' separated strings
*/
-
- groupURLLinks = new Vector();
- groupURLLinks.addElement("UNIPROT|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=Default&datasetName=JalviewIDs$DATASETID$&input=$SEQUENCEIDS$&inputType=0|,");
- // TODO: make sequence Group URL links more efficiently generated so popup menu does not take so long.
- // groupURLLinks.addElement("Seqs|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=Default&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCES=/([A-Za-z]+)+/=$&inputType=1|,");
-
- }
- Vector nameLinks, urlLinks;
+ groupURLLinks = new ArrayList<>(); // not implemented
+ }
JInternalFrame frame;
- DasSourceBrowser dasSource;
+ private WsPreferences wsPrefs;
+
+ private OptionsParam promptEachTimeOpt = new OptionsParam(
+ MessageManager.getString("label.prompt_each_time"),
+ "Prompt each time");
+
+ private OptionsParam lineArtOpt = new OptionsParam(
+ MessageManager.getString("label.lineart"), "Lineart");
+
+ private OptionsParam textOpt = new OptionsParam(
+ MessageManager.getString("action.text"), "Text");
/**
* Creates a new Preferences object.
*/
public Preferences()
{
-
+ super();
frame = new JInternalFrame();
frame.setContentPane(this);
- dasSource = new DasSourceBrowser();
- dasPanel.add(dasSource, BorderLayout.CENTER);
-
- int width = 500, height = 420;
- if (new jalview.util.Platform().isAMac())
+ if (!Platform.isJS())
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
{
- width = 570;
- height = 460;
+ wsPrefs = new WsPreferences();
+ wsTab.add(wsPrefs, BorderLayout.CENTER);
}
-
- Desktop.addInternalFrame(frame, "Preferences", width, height);
- frame.setMinimumSize(new Dimension(width, height));
-
- seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
- rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
- fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
- annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
-
- conservation.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
- quality.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
- identity.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
-
- conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
- quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
- identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
- openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
- showUnconserved.setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
-
- for (int i = 0; i < 13; i++)
+ int width = 500, height = 510; // BH 2019.07.12 added 60 to height
+ // (structure panel was too small anyway, and I added a default dimension
+ // for Jmol
+ if (Platform.isAMacAndNotJS())
{
- colour.addItem(ColourSchemeProperty.getColourName(i));
+ width = 570;
+ height = 540; // BH 2019.07.12 added 30
}
- String string = Cache.getDefault("DEFAULT_COLOUR", "None");
+ Desktop.addInternalFrame(frame,
+ MessageManager.getString("label.preferences"), width, height);
+ frame.setMinimumSize(new Dimension(width, height));
- colour.setSelectedItem(string);
+ /*
+ * Set Visual tab defaults
+ */
+ seqLimit.setSelected(Cache.getDefault(SHOW_JVSUFFIX, true));
+ rightAlign.setSelected(Cache.getDefault(RIGHT_ALIGN_IDS, false));
+ fullScreen.setSelected(Cache.getDefault(SHOW_FULLSCREEN, false));
+ annotations.setSelected(Cache.getDefault(SHOW_ANNOTATIONS, true));
+
+ conservation.setSelected(Cache.getDefault(SHOW_CONSERVATION, true));
+ quality.setSelected(Cache.getDefault(SHOW_QUALITY, true));
+ identity.setSelected(Cache.getDefault(SHOW_IDENTITY, true));
+ openoverv.setSelected(Cache.getDefault(SHOW_OVERVIEW, false));
+ showUnconserved
+ .setSelected(Cache.getDefault(SHOW_UNCONSERVED, false));
+ showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
+ showGroupConsensus
+ .setSelected(Cache.getDefault(SHOW_GROUP_CONSENSUS, false));
+ showGroupConservation.setSelected(
+ Cache.getDefault(SHOW_GROUP_CONSERVATION, false));
+ showConsensHistogram.setSelected(
+ Cache.getDefault(SHOW_CONSENSUS_HISTOGRAM, true));
+ showConsensLogo
+ .setSelected(Cache.getDefault(SHOW_CONSENSUS_LOGO, false));
+ showNpTooltip
+ .setSelected(Cache.getDefault(SHOW_NPFEATS_TOOLTIP, true));
+ showDbRefTooltip
+ .setSelected(Cache.getDefault(SHOW_DBREFS_TOOLTIP, true));
String[] fonts = java.awt.GraphicsEnvironment
.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
-
for (int i = 0; i < fonts.length; i++)
{
fontNameCB.addItem(fonts[i]);
}
- for (int i = 1; i < 31; i++)
+ for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
{
fontSizeCB.addItem(i + "");
}
@@ -158,208 +363,524 @@ public class Preferences extends GPreferences
fontStyleCB.addItem("bold");
fontStyleCB.addItem("italic");
- fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
- fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
- fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN
- + ""));
+ fontNameCB.setSelectedItem(Cache.getDefault(FONT_NAME, "SansSerif"));
+ fontSizeCB.setSelectedItem(Cache.getDefault(FONT_SIZE, "10"));
+ fontStyleCB.setSelectedItem(
+ Cache.getDefault(FONT_STYLE, Font.PLAIN + ""));
- smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
+ smoothFont.setSelected(Cache.getDefault(ANTI_ALIAS, false));
+ scaleProteinToCdna
+ .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
- idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
+ idItalics.setSelected(Cache.getDefault(ID_ITALICS, true));
- wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
+ wrap.setSelected(Cache.getDefault(WRAP_ALIGNMENT, false));
gapSymbolCB.addItem("-");
gapSymbolCB.addItem(".");
- gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
+ gapSymbolCB.setSelectedItem(Cache.getDefault(GAP_SYMBOL, "-"));
+ sortby.addItem("No sort");
+ sortby.addItem("Id");
+ sortby.addItem("Pairwise Identity");
+ sortby.setSelectedItem(Cache.getDefault(SORT_ALIGNMENT, "No sort"));
+
+ sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
+ sortAnnBy
+ .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
+ sortAnnBy
+ .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
+ SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
+ .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
+ SequenceAnnotationOrder.NONE.name()));
+ sortAnnBy.setSelectedItem(savedSort.toString());
+
+ sortAutocalc.addItem("Autocalculated first");
+ sortAutocalc.addItem("Autocalculated last");
+ final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
+ sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
+ : sortAutocalc.getItemAt(1));
startupCheckbox
.setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
- "http://www.jalview.org/examples/exampleFile_2_3.jar"));
+ Cache.getDefault("www.jalview.org", "http://www.jalview.org")
+ + "/examples/exampleFile_2_3.jar"));
- sortby.addItem("No sort");
- sortby.addItem("Id");
- sortby.addItem("Pairwise Identity");
- sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
+ /*
+ * Set Colours tab defaults
+ */
+ protColour.addItem(ResidueColourScheme.NONE);
+ nucColour.addItem(ResidueColourScheme.NONE);
+ for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
+ {
+ String name = cs.getSchemeName();
+ protColour.addItem(name);
+ nucColour.addItem(name);
+ }
+ String oldProp = Cache.getDefault(DEFAULT_COLOUR,
+ ResidueColourScheme.NONE);
+ String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
+ protColour.setSelectedItem(newProp != null ? newProp : oldProp);
+ newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
+ nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
+ minColour.setBackground(
+ Cache.getDefaultColour(ANNOTATIONCOLOUR_MIN, Color.orange));
+ maxColour.setBackground(
+ Cache.getDefaultColour(ANNOTATIONCOLOUR_MAX, Color.red));
+
+ /*
+ * Set overview panel defaults
+ */
+ gapColour.setBackground(
+ Cache.getDefaultColour(GAP_COLOUR,
+ jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP));
+ hiddenColour.setBackground(
+ Cache.getDefaultColour(HIDDEN_COLOUR,
+ jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN));
+ useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
+ gapLabel.setEnabled(!useLegacyGap.isSelected());
+ gapColour.setEnabled(!useLegacyGap.isSelected());
+ showHiddenAtStart
+ .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, false));
+
+ /*
+ * Set Structure tab defaults.
+ */
+ final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
+ structFromPdb.setSelected(structSelected);
+ useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
+ useRnaView.setEnabled(structSelected);
+ addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
+ addSecondaryStructure.setEnabled(structSelected);
+ addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
+ addTempFactor.setEnabled(structSelected);
+ structViewer.setSelectedItem(
+ Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name()));
+ Dimension d = Cache.getDefaultDim(STRUCTURE_DIMENSIONS,
+ DEFAULT_STRUCTURE_DIMENSIONS);
+ String s = d.width + "," + d.height;
+ structureDimensions.setText(s);
+ chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
+ chimeraPath.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ validateChimeraPath();
+ }
+ });
+
+ if (Cache.getDefault(MAP_WITH_SIFTS, false))
+ {
+ siftsMapping.setSelected(true);
+ }
+ else
+ {
+ nwMapping.setSelected(true);
+ }
- epsRendering.addItem("Prompt each time");
- epsRendering.addItem("Lineart");
- epsRendering.addItem("Text");
- epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING",
- "Prompt each time"));
+ SiftsSettings
+ .setMapWithSifts(Cache.getDefault(MAP_WITH_SIFTS, false));
- blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
- clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
- fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
- msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
- pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
- pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
- pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
+ /*
+ * Set Connections tab defaults
+ */
- modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
+ // set up sorting
+ linkUrlTable.setModel(dataModel);
+ final TableRowSorter sorter = new TableRowSorter<>(
+ linkUrlTable.getModel());
+ linkUrlTable.setRowSorter(sorter);
+ List sortKeys = new ArrayList<>();
+
+ UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
+ sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
+ SortOrder.DESCENDING));
+ sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
+ SortOrder.DESCENDING));
+ sortKeys.add(
+ new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
+
+ sorter.setSortKeys(sortKeys);
+ // BH 2018 setSortKeys will do the sort
+ // sorter.sort();
+
+ // set up filtering
+ ActionListener onReset;
+ onReset = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ filterTB.setText("");
+ sorter.setRowFilter(RowFilter.regexFilter(""));
+ }
- autoCalculateConsCheck.setSelected(Cache.getDefault(
- "AUTO_CALC_CONSENSUS", true));
- padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
+ };
+ doReset.addActionListener(onReset);
- /***************************************************************************
- * Set up Connections
- */
- nameLinks = new Vector();
- urlLinks = new Vector();
- for (int i = 0; i < sequenceURLLinks.size(); i++)
+ // filter to display only custom urls
+ final RowFilter customUrlFilter = new RowFilter()
{
- String link = sequenceURLLinks.elementAt(i).toString();
- nameLinks.addElement(link.substring(0, link.indexOf("|")));
- urlLinks.addElement(link.substring(link.indexOf("|") + 1));
- }
+ @Override
+ public boolean include(
+ Entry extends TableModel, ? extends Object> entry)
+ {
+ return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry);
+ }
+ };
+
+ final TableRowSorter customSorter = new TableRowSorter<>(
+ linkUrlTable.getModel());
+ customSorter.setRowFilter(customUrlFilter);
+
+ ActionListener onCustomOnly;
+ onCustomOnly = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ filterTB.setText("");
+ sorter.setRowFilter(customUrlFilter);
+ }
+ };
+ userOnly.addActionListener(onCustomOnly);
- updateLinkData();
+ filterTB.getDocument().addDocumentListener(new DocumentListener()
+ {
+ String caseInsensitiveFlag = "(?i)";
+
+ @Override
+ public void changedUpdate(DocumentEvent e)
+ {
+ sorter.setRowFilter(RowFilter
+ .regexFilter(caseInsensitiveFlag + filterTB.getText()));
+ }
+
+ @Override
+ public void removeUpdate(DocumentEvent e)
+ {
+ sorter.setRowFilter(RowFilter
+ .regexFilter(caseInsensitiveFlag + filterTB.getText()));
+ }
+
+ @Override
+ public void insertUpdate(DocumentEvent e)
+ {
+ sorter.setRowFilter(RowFilter
+ .regexFilter(caseInsensitiveFlag + filterTB.getText()));
+ }
+ });
+
+ // set up list selection functionality
+ linkUrlTable.getSelectionModel()
+ .addListSelectionListener(new UrlListSelectionHandler());
+
+ // set up radio buttons
+ int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
+ .getPrimaryColumn();
+ String onClickName = linkUrlTable.getColumnName(onClickCol);
+ linkUrlTable.getColumn(onClickName)
+ .setCellRenderer(new RadioButtonRenderer());
+ linkUrlTable.getColumn(onClickName)
+ .setCellEditor(new RadioButtonEditor());
+
+ // get boolean columns and resize those to min possible
+ for (int column = 0; column < linkUrlTable.getColumnCount(); column++)
+ {
+ if (linkUrlTable.getModel().getColumnClass(column)
+ .equals(Boolean.class))
+ {
+ TableColumn tableColumn = linkUrlTable.getColumnModel()
+ .getColumn(column);
+ int preferredWidth = tableColumn.getMinWidth();
+
+ TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
+ column);
+ Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column);
+ int cwidth = c.getPreferredSize().width
+ + linkUrlTable.getIntercellSpacing().width;
+ preferredWidth = Math.max(preferredWidth, cwidth);
+
+ tableColumn.setPreferredWidth(preferredWidth);
+ }
+ }
useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
- proxyServerTB.setEnabled(useProxy.isSelected());
- proxyPortTB.setEnabled(useProxy.isSelected());
+ useProxy_actionPerformed(); // make sure useProxy is correctly initialised
proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
-
+
usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
- questionnaire.setSelected(Cache.getProperty("NOQUESTIONNAIRES")==null); // note antisense here
- versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true)); // default is true
+ // note antisense here: default is true
+ questionnaire
+ .setSelected(Cache.getProperty(NOQUESTIONNAIRES) == null);
+ versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
- try
+ /*
+ * Set Output tab defaults
+ */
+ setupOutputCombo(epsRendering, "EPS_RENDERING");
+ setupOutputCombo(htmlRendering, "HTML_RENDERING");
+ setupOutputCombo(svgRendering, "SVG_RENDERING");
+ autoIdWidth.setSelected(Cache.getDefault(FIGURE_AUTOIDWIDTH, false));
+ userIdWidth.setEnabled(!autoIdWidth.isSelected());
+ userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
+ Integer wi = Cache.getIntegerProperty(FIGURE_FIXEDIDWIDTH);
+ userIdWidth.setText(wi == null ? "" : wi.toString());
+ // TODO: refactor to use common enum via FormatAdapter and allow extension
+ // for new flat file formats
+ blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
+ clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
+ fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
+ msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
+ pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
+ pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
+ pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
+ modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
+ embbedBioJSON
+ .setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true));
+
+ /*
+ * Set Editing tab defaults
+ */
+ autoCalculateConsCheck
+ .setSelected(Cache.getDefault(AUTO_CALC_CONSENSUS, true));
+ padGaps.setSelected(Cache.getDefault(PAD_GAPS, false));
+ sortByTree.setSelected(Cache.getDefault(SORT_BY_TREE, false));
+
+ annotations_actionPerformed(null); // update the display of the annotation
+ // settings
+
+
+ /*
+ * Set Backups tab defaults
+ */
+ loadLastSavedBackupsOptions();
+ }
+
+ /**
+ * A helper method that sets the items and initial selection in a character
+ * rendering option list (Prompt each time/Lineart/Text)
+ *
+ * @param comboBox
+ * @param propertyKey
+ */
+ protected void setupOutputCombo(JComboBox